Contents

Jupyter Notebook files

Use minnie_plotly_and_vtk_visualizer.ipynb to generate a 2D and 3D interactive views of one or more cells of interest from the minnie mm^3 volume. Uses matplotlib, plotly, and vtk/openGL visualization methods. See an example visualization below.

vtk visualization of neurons in the minnie volume

Use pyvista_decimate_mesh_cell_bodies_minnie.ipynb to decimate cell meshes from the minnie volume. Default decimation setting is 95%. You must first download the meshes to your local drive using the minnie_plotly_and_vtk_visualizer.ipynb notebook. Decimated files will be saved in the ‘/dec’ subdirectory. Note that astrocyte meshes may take several hours to decimate. Most other cell types will only take minutes.

Use vtk_decimated_cell_meshes_minnie.ipynb to generate a 3D interactive view of one or more cells of interest using decimated meshes from the minnie mm^3 volume. Uses vtk/openGL and has a save view function. See an example visualization below.

vtk visualization of decimated meshes of astrocytes, neurons, and vascular cells in the minnie volume